Generate a sample-by-component matrix

This function generate a sample-by-component matrix representing the sum of posterior probabilities of each copy-number event being assigned to each component.

cnv_generateSbCMatrix(CN_features, all_components = NULL, cores = 1,
  rowIter = 1000)

Arguments

CN_features	a list contains six copy number feature distributions, obtain this from cnv_derivefeatures function.
all_components	a list contain flexmix object of copy-number features, obtain this from cnv_fitMixModels function or use pre-compiled components data which come from CNV signature paper https://www.nature.com/articles/s41588-018-0179-8 (set this argument as NULL).
cores	number of compute cores to run this task. You can use detectCores function to check how many cores you can use. If you are using cnv_pipe feature, please do not use maximal number of cores in your computer, it may cause some unexpected problems.
rowIter	step size of iteration for rows of ech CNV feature data.frame.

Value

a numeric sample-by-component matrix

Examples

# NOT RUN {
## load example copy-number data from tcga
load(system.file("inst/extdata", "example_cn_list.RData", package = "VSHunter"))
## generate copy-number features
tcga_features = cnv_derivefeatures(CN_data = tcga_segTabs, cores = 1, genome_build = "hg19")
## fit mixture model  (this will take some time)
tcga_components = cnv_fitMixModels(CN_features = tcga_features, cores = 1)
## generate a sample-by-component matrix
tcga_sample_component_matrix = cnv_generateSbCMatrix(tcga_features, tcga_components, cores = 1)
# }